Starting phenix.real_space_refine on Sat Mar 16 14:22:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3r_29709/03_2024/8g3r_29709.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3r_29709/03_2024/8g3r_29709.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3r_29709/03_2024/8g3r_29709.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3r_29709/03_2024/8g3r_29709.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3r_29709/03_2024/8g3r_29709.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3r_29709/03_2024/8g3r_29709.pdb" } resolution = 2.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.039 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 5 9.91 5 S 95 5.16 5 C 9192 2.51 5 N 2500 2.21 5 O 3107 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E ARG 85": "NH1" <-> "NH2" Residue "E ARG 107": "NH1" <-> "NH2" Residue "E ARG 118": "NH1" <-> "NH2" Residue "E ARG 150": "NH1" <-> "NH2" Residue "E ARG 152": "NH1" <-> "NH2" Residue "E ARG 156": "NH1" <-> "NH2" Residue "E ARG 210": "NH1" <-> "NH2" Residue "E ARG 224": "NH1" <-> "NH2" Residue "E TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 283": "NH1" <-> "NH2" Residue "E ARG 288": "NH1" <-> "NH2" Residue "E ARG 292": "NH1" <-> "NH2" Residue "E ARG 300": "NH1" <-> "NH2" Residue "E ARG 327": "NH1" <-> "NH2" Residue "E PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 364": "NH1" <-> "NH2" Residue "E ARG 371": "NH1" <-> "NH2" Residue "E ARG 394": "NH1" <-> "NH2" Residue "E ARG 400": "NH1" <-> "NH2" Residue "E ARG 403": "NH1" <-> "NH2" Residue "E ARG 420": "NH1" <-> "NH2" Residue "E ARG 428": "NH1" <-> "NH2" Residue "E ARG 430": "NH1" <-> "NH2" Residue "G ARG 85": "NH1" <-> "NH2" Residue "G ARG 107": "NH1" <-> "NH2" Residue "G ARG 118": "NH1" <-> "NH2" Residue "G PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 150": "NH1" <-> "NH2" Residue "G ARG 152": "NH1" <-> "NH2" Residue "G ARG 156": "NH1" <-> "NH2" Residue "G ARG 210": "NH1" <-> "NH2" Residue "G ARG 224": "NH1" <-> "NH2" Residue "G TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 283": "NH1" <-> "NH2" Residue "G ARG 288": "NH1" <-> "NH2" Residue "G ARG 292": "NH1" <-> "NH2" Residue "G ARG 300": "NH1" <-> "NH2" Residue "G ARG 327": "NH1" <-> "NH2" Residue "G PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 364": "NH1" <-> "NH2" Residue "G ARG 371": "NH1" <-> "NH2" Residue "G ARG 394": "NH1" <-> "NH2" Residue "G ARG 400": "NH1" <-> "NH2" Residue "G ARG 403": "NH1" <-> "NH2" Residue "G ARG 420": "NH1" <-> "NH2" Residue "G ARG 428": "NH1" <-> "NH2" Residue "G ARG 430": "NH1" <-> "NH2" Residue "B ARG 18": "NH1" <-> "NH2" Residue "B ARG 24": "NH1" <-> "NH2" Residue "B ARG 45": "NH1" <-> "NH2" Residue "B ARG 54": "NH1" <-> "NH2" Residue "B ARG 61": "NH1" <-> "NH2" Residue "B ARG 109": "NH1" <-> "NH2" Residue "C ARG 13": "NH1" <-> "NH2" Residue "C ARG 38": "NH1" <-> "NH2" Residue "C ARG 67": "NH1" <-> "NH2" Residue "C ARG 87": "NH1" <-> "NH2" Residue "C ARG 98": "NH1" <-> "NH2" Residue "C ARG 100": "NH1" <-> "NH2" Residue "C ARG 106": "NH1" <-> "NH2" Residue "F ARG 85": "NH1" <-> "NH2" Residue "F ARG 107": "NH1" <-> "NH2" Residue "F ARG 118": "NH1" <-> "NH2" Residue "F PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 150": "NH1" <-> "NH2" Residue "F ARG 152": "NH1" <-> "NH2" Residue "F ARG 156": "NH1" <-> "NH2" Residue "F ARG 210": "NH1" <-> "NH2" Residue "F ARG 224": "NH1" <-> "NH2" Residue "F TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 283": "NH1" <-> "NH2" Residue "F ARG 288": "NH1" <-> "NH2" Residue "F ARG 292": "NH1" <-> "NH2" Residue "F ARG 300": "NH1" <-> "NH2" Residue "F ARG 327": "NH1" <-> "NH2" Residue "F ARG 364": "NH1" <-> "NH2" Residue "F ARG 371": "NH1" <-> "NH2" Residue "F ARG 394": "NH1" <-> "NH2" Residue "F ARG 400": "NH1" <-> "NH2" Residue "F ARG 403": "NH1" <-> "NH2" Residue "F ARG 420": "NH1" <-> "NH2" Residue "F ARG 428": "NH1" <-> "NH2" Residue "F ARG 430": "NH1" <-> "NH2" Residue "H ARG 85": "NH1" <-> "NH2" Residue "H ARG 107": "NH1" <-> "NH2" Residue "H ARG 118": "NH1" <-> "NH2" Residue "H ARG 150": "NH1" <-> "NH2" Residue "H ARG 152": "NH1" <-> "NH2" Residue "H ARG 156": "NH1" <-> "NH2" Residue "H ARG 210": "NH1" <-> "NH2" Residue "H ARG 224": "NH1" <-> "NH2" Residue "H TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 283": "NH1" <-> "NH2" Residue "H ARG 288": "NH1" <-> "NH2" Residue "H ARG 292": "NH1" <-> "NH2" Residue "H ARG 300": "NH1" <-> "NH2" Residue "H ARG 327": "NH1" <-> "NH2" Residue "H PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 364": "NH1" <-> "NH2" Residue "H ARG 371": "NH1" <-> "NH2" Residue "H ARG 394": "NH1" <-> "NH2" Residue "H ARG 400": "NH1" <-> "NH2" Residue "H ARG 403": "NH1" <-> "NH2" Residue "H ARG 420": "NH1" <-> "NH2" Residue "H ARG 428": "NH1" <-> "NH2" Residue "H ARG 430": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 14899 Number of models: 1 Model: "" Number of chains: 38 Chain: "E" Number of atoms: 3004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3004 Classifications: {'peptide': 388} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 12, 'TRANS': 372} Chain: "G" Number of atoms: 3004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3004 Classifications: {'peptide': 388} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 12, 'TRANS': 372} Chain: "B" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 834 Classifications: {'peptide': 109} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 101} Chain: "C" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 986 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 4, 'TRANS': 124} Chain: "F" Number of atoms: 3004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3004 Classifications: {'peptide': 388} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 12, 'TRANS': 372} Chain: "H" Number of atoms: 3004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3004 Classifications: {'peptide': 388} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 12, 'TRANS': 372} Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "d" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "r" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "s" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "t" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "v" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "w" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "1" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "2" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "3" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "4" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "6" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "7" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "u" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "5" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.76, per 1000 atoms: 0.52 Number of scatterers: 14899 At special positions: 0 Unit cell: (97.94, 119.52, 144.42, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 5 19.99 S 95 16.00 O 3107 8.00 N 2500 7.00 C 9192 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, symmetry=0 Simple disulfide: pdb=" SG CYS E 92 " - pdb=" SG CYS E 417 " distance=2.04 Simple disulfide: pdb=" SG CYS E 124 " - pdb=" SG CYS E 129 " distance=2.08 Simple disulfide: pdb=" SG CYS E 175 " - pdb=" SG CYS E 193 " distance=2.00 Simple disulfide: pdb=" SG CYS E 183 " - pdb=" SG CYS E 230 " distance=2.06 Simple disulfide: pdb=" SG CYS E 232 " - pdb=" SG CYS E 237 " distance=2.10 Simple disulfide: pdb=" SG CYS E 278 " - pdb=" SG CYS E 291 " distance=2.11 Simple disulfide: pdb=" SG CYS E 280 " - pdb=" SG CYS E 289 " distance=2.08 Simple disulfide: pdb=" SG CYS E 318 " - pdb=" SG CYS E 337 " distance=2.07 Simple disulfide: pdb=" SG CYS E 421 " - pdb=" SG CYS E 447 " distance=2.16 Simple disulfide: pdb=" SG CYS G 92 " - pdb=" SG CYS G 417 " distance=2.04 Simple disulfide: pdb=" SG CYS G 124 " - pdb=" SG CYS G 129 " distance=2.09 Simple disulfide: pdb=" SG CYS G 175 " - pdb=" SG CYS G 193 " distance=2.04 Simple disulfide: pdb=" SG CYS G 183 " - pdb=" SG CYS G 230 " distance=2.06 Simple disulfide: pdb=" SG CYS G 232 " - pdb=" SG CYS G 237 " distance=2.09 Simple disulfide: pdb=" SG CYS G 278 " - pdb=" SG CYS G 291 " distance=2.09 Simple disulfide: pdb=" SG CYS G 280 " - pdb=" SG CYS G 289 " distance=2.08 Simple disulfide: pdb=" SG CYS G 318 " - pdb=" SG CYS G 337 " distance=2.09 Simple disulfide: pdb=" SG CYS G 421 " - pdb=" SG CYS G 447 " distance=2.15 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.05 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.02 Simple disulfide: pdb=" SG CYS F 92 " - pdb=" SG CYS F 417 " distance=2.05 Simple disulfide: pdb=" SG CYS F 124 " - pdb=" SG CYS F 129 " distance=2.08 Simple disulfide: pdb=" SG CYS F 175 " - pdb=" SG CYS F 193 " distance=2.02 Simple disulfide: pdb=" SG CYS F 183 " - pdb=" SG CYS F 230 " distance=2.07 Simple disulfide: pdb=" SG CYS F 232 " - pdb=" SG CYS F 237 " distance=2.10 Simple disulfide: pdb=" SG CYS F 278 " - pdb=" SG CYS F 291 " distance=2.12 Simple disulfide: pdb=" SG CYS F 280 " - pdb=" SG CYS F 289 " distance=2.09 Simple disulfide: pdb=" SG CYS F 318 " - pdb=" SG CYS F 337 " distance=2.08 Simple disulfide: pdb=" SG CYS F 421 " - pdb=" SG CYS F 447 " distance=2.13 Simple disulfide: pdb=" SG CYS H 92 " - pdb=" SG CYS H 417 " distance=2.04 Simple disulfide: pdb=" SG CYS H 124 " - pdb=" SG CYS H 129 " distance=2.09 Simple disulfide: pdb=" SG CYS H 175 " - pdb=" SG CYS H 193 " distance=2.04 Simple disulfide: pdb=" SG CYS H 183 " - pdb=" SG CYS H 230 " distance=2.07 Simple disulfide: pdb=" SG CYS H 232 " - pdb=" SG CYS H 237 " distance=2.10 Simple disulfide: pdb=" SG CYS H 278 " - pdb=" SG CYS H 291 " distance=2.09 Simple disulfide: pdb=" SG CYS H 280 " - pdb=" SG CYS H 289 " distance=2.08 Simple disulfide: pdb=" SG CYS H 318 " - pdb=" SG CYS H 337 " distance=2.08 Simple disulfide: pdb=" SG CYS H 421 " - pdb=" SG CYS H 447 " distance=2.13 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN 3 4 " - " MAN 3 5 " " MAN c 4 " - " MAN c 5 " " MAN k 4 " - " MAN k 5 " " MAN s 4 " - " MAN s 5 " ALPHA1-3 " BMA 3 3 " - " MAN 3 4 " " MAN 3 6 " - " MAN 3 7 " " BMA c 3 " - " MAN c 4 " " MAN c 6 " - " MAN c 7 " " BMA k 3 " - " MAN k 4 " " MAN k 6 " - " MAN k 7 " " BMA s 3 " - " MAN s 4 " " MAN s 6 " - " MAN s 7 " ALPHA1-6 " BMA 3 3 " - " MAN 3 6 " " MAN 3 6 " - " MAN 3 8 " " BMA c 3 " - " MAN c 6 " " MAN c 6 " - " MAN c 8 " " BMA k 3 " - " MAN k 6 " " MAN k 6 " - " MAN k 8 " " BMA s 3 " - " MAN s 6 " " MAN s 6 " - " MAN s 8 " BETA1-4 " NAG 1 1 " - " NAG 1 2 " " NAG 2 1 " - " NAG 2 2 " " NAG 3 1 " - " NAG 3 2 " " NAG 3 2 " - " BMA 3 3 " " NAG 4 1 " - " NAG 4 2 " " NAG 5 1 " - " NAG 5 2 " " NAG 6 1 " - " NAG 6 2 " " NAG 7 1 " - " NAG 7 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " " NAG t 1 " - " NAG t 2 " " NAG u 1 " - " NAG u 2 " " NAG v 1 " - " NAG v 2 " " NAG w 1 " - " NAG w 2 " BETA1-6 " NAG d 1 " - " FUC d 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG 1 1 " - " ASN H 86 " " NAG 2 1 " - " ASN H 146 " " NAG 3 1 " - " ASN H 200 " " NAG 4 1 " - " ASN H 234 " " NAG 5 1 " - " ASN H 245 " " NAG 6 1 " - " ASN H 329 " " NAG 7 1 " - " ASN H 367 " " NAG a 1 " - " ASN E 86 " " NAG b 1 " - " ASN E 146 " " NAG c 1 " - " ASN E 200 " " NAG d 1 " - " ASN E 234 " " NAG e 1 " - " ASN E 245 " " NAG f 1 " - " ASN E 329 " " NAG g 1 " - " ASN E 367 " " NAG i 1 " - " ASN F 86 " " NAG j 1 " - " ASN F 146 " " NAG k 1 " - " ASN F 200 " " NAG l 1 " - " ASN F 234 " " NAG m 1 " - " ASN F 245 " " NAG n 1 " - " ASN F 329 " " NAG o 1 " - " ASN F 367 " " NAG q 1 " - " ASN G 86 " " NAG r 1 " - " ASN G 146 " " NAG s 1 " - " ASN G 200 " " NAG t 1 " - " ASN G 234 " " NAG u 1 " - " ASN G 245 " " NAG v 1 " - " ASN G 329 " " NAG w 1 " - " ASN G 367 " Time building additional restraints: 6.36 Conformation dependent library (CDL) restraints added in 2.3 seconds 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3238 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 30 sheets defined 3.7% alpha, 41.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.24 Creating SS restraints... Processing helix chain 'E' and resid 104 through 110 removed outlier: 3.539A pdb=" N ALA E 110 " --> pdb=" O ILE E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 142 through 146 Processing helix chain 'G' and resid 104 through 110 Processing helix chain 'G' and resid 142 through 146 Processing helix chain 'G' and resid 247 through 251 Processing helix chain 'B' and resid 79 through 83 removed outlier: 3.903A pdb=" N PHE B 83 " --> pdb=" O SER B 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 65 Processing helix chain 'C' and resid 87 through 91 Processing helix chain 'F' and resid 104 through 110 removed outlier: 3.548A pdb=" N ALA F 110 " --> pdb=" O ILE F 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 142 through 146 Processing helix chain 'H' and resid 104 through 110 removed outlier: 3.535A pdb=" N ALA H 110 " --> pdb=" O ILE H 106 " (cutoff:3.500A) Processing helix chain 'H' and resid 142 through 146 Processing sheet with id=AA1, first strand: chain 'E' and resid 96 through 102 removed outlier: 3.724A pdb=" N GLY E 96 " --> pdb=" O THR E 449 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL E 445 " --> pdb=" O PHE E 100 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N LYS E 102 " --> pdb=" O ILE E 443 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N ILE E 443 " --> pdb=" O LYS E 102 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N ARG E 420 " --> pdb=" O GLY E 448 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 115 through 124 removed outlier: 4.697A pdb=" N TRP E 115 " --> pdb=" O THR E 138 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N THR E 138 " --> pdb=" O TRP E 115 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N THR E 117 " --> pdb=" O GLN E 136 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N GLN E 136 " --> pdb=" O THR E 117 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N GLU E 119 " --> pdb=" O LEU E 134 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LEU E 134 " --> pdb=" O GLU E 119 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N THR E 157 " --> pdb=" O GLY E 135 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N LEU E 158 " --> pdb=" O VAL E 174 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LYS E 172 " --> pdb=" O MET E 160 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 179 through 184 removed outlier: 4.108A pdb=" N ASP E 197 " --> pdb=" O ASN E 200 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ALA E 201 " --> pdb=" O VAL E 216 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N VAL E 216 " --> pdb=" O ALA E 201 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ALA E 203 " --> pdb=" O SER E 214 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N SER E 214 " --> pdb=" O ALA E 203 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N PHE E 205 " --> pdb=" O VAL E 212 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 231 through 233 removed outlier: 6.523A pdb=" N GLU E 258 " --> pdb=" O ILE E 262 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N ILE E 262 " --> pdb=" O GLU E 258 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 276 through 283 removed outlier: 5.405A pdb=" N GLU E 277 " --> pdb=" O ARG E 292 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N ARG E 292 " --> pdb=" O GLU E 277 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 353 through 356 removed outlier: 7.067A pdb=" N ASN E 402 " --> pdb=" O GLY E 373 " (cutoff:3.500A) removed outlier: 9.802A pdb=" N GLU E 375 " --> pdb=" O ARG E 400 " (cutoff:3.500A) removed outlier: 10.518A pdb=" N ARG E 400 " --> pdb=" O GLU E 375 " (cutoff:3.500A) removed outlier: 11.375A pdb=" N PHE E 377 " --> pdb=" O VAL E 398 " (cutoff:3.500A) removed outlier: 13.437A pdb=" N VAL E 398 " --> pdb=" O PHE E 377 " (cutoff:3.500A) removed outlier: 15.480A pdb=" N VAL E 379 " --> pdb=" O VAL E 396 " (cutoff:3.500A) removed outlier: 16.202A pdb=" N VAL E 396 " --> pdb=" O VAL E 379 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 96 through 102 removed outlier: 3.691A pdb=" N GLY G 96 " --> pdb=" O THR G 449 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N VAL G 445 " --> pdb=" O PHE G 100 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N LYS G 102 " --> pdb=" O ILE G 443 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ILE G 443 " --> pdb=" O LYS G 102 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N ARG G 420 " --> pdb=" O GLY G 448 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 115 through 124 removed outlier: 4.696A pdb=" N TRP G 115 " --> pdb=" O THR G 138 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N THR G 138 " --> pdb=" O TRP G 115 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N THR G 117 " --> pdb=" O GLN G 136 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N GLN G 136 " --> pdb=" O THR G 117 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N GLU G 119 " --> pdb=" O LEU G 134 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LEU G 134 " --> pdb=" O GLU G 119 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR G 157 " --> pdb=" O GLY G 135 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N LEU G 158 " --> pdb=" O VAL G 174 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LYS G 172 " --> pdb=" O MET G 160 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 179 through 184 removed outlier: 4.070A pdb=" N ASP G 197 " --> pdb=" O ASN G 200 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ALA G 201 " --> pdb=" O VAL G 216 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N VAL G 216 " --> pdb=" O ALA G 201 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ALA G 203 " --> pdb=" O SER G 214 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N SER G 214 " --> pdb=" O ALA G 203 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N PHE G 205 " --> pdb=" O VAL G 212 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 231 through 233 removed outlier: 3.514A pdb=" N VAL G 231 " --> pdb=" O THR G 238 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N GLU G 258 " --> pdb=" O ILE G 262 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N ILE G 262 " --> pdb=" O GLU G 258 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 276 through 283 removed outlier: 5.376A pdb=" N GLU G 277 " --> pdb=" O ARG G 292 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ARG G 292 " --> pdb=" O GLU G 277 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 353 through 356 removed outlier: 7.043A pdb=" N ASN G 402 " --> pdb=" O GLY G 373 " (cutoff:3.500A) removed outlier: 9.743A pdb=" N GLU G 375 " --> pdb=" O ARG G 400 " (cutoff:3.500A) removed outlier: 10.525A pdb=" N ARG G 400 " --> pdb=" O GLU G 375 " (cutoff:3.500A) removed outlier: 11.392A pdb=" N PHE G 377 " --> pdb=" O VAL G 398 " (cutoff:3.500A) removed outlier: 13.449A pdb=" N VAL G 398 " --> pdb=" O PHE G 377 " (cutoff:3.500A) removed outlier: 15.466A pdb=" N VAL G 379 " --> pdb=" O VAL G 396 " (cutoff:3.500A) removed outlier: 16.192A pdb=" N VAL G 396 " --> pdb=" O VAL G 379 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 4 through 7 removed outlier: 3.716A pdb=" N GLU B 70 " --> pdb=" O SER B 67 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 10 through 13 removed outlier: 6.589A pdb=" N LEU B 33 " --> pdb=" O TYR B 49 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N TYR B 49 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 4 through 6 Processing sheet with id=AB7, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.240A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.800A pdb=" N CYS C 96 " --> pdb=" O TRP C 118 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N TRP C 118 " --> pdb=" O CYS C 96 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ARG C 98 " --> pdb=" O GLU C 116 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 104 through 105 Processing sheet with id=AC1, first strand: chain 'F' and resid 96 through 102 removed outlier: 3.704A pdb=" N GLY F 96 " --> pdb=" O THR F 449 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VAL F 445 " --> pdb=" O PHE F 100 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N LYS F 102 " --> pdb=" O ILE F 443 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N ILE F 443 " --> pdb=" O LYS F 102 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N ARG F 420 " --> pdb=" O GLY F 448 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 115 through 124 removed outlier: 4.689A pdb=" N TRP F 115 " --> pdb=" O THR F 138 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N THR F 138 " --> pdb=" O TRP F 115 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N THR F 117 " --> pdb=" O GLN F 136 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N GLN F 136 " --> pdb=" O THR F 117 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N GLU F 119 " --> pdb=" O LEU F 134 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEU F 134 " --> pdb=" O GLU F 119 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR F 157 " --> pdb=" O GLY F 135 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LEU F 158 " --> pdb=" O VAL F 174 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LYS F 172 " --> pdb=" O MET F 160 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 179 through 184 removed outlier: 4.106A pdb=" N ASP F 197 " --> pdb=" O ASN F 200 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ALA F 201 " --> pdb=" O VAL F 216 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N VAL F 216 " --> pdb=" O ALA F 201 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ALA F 203 " --> pdb=" O SER F 214 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N SER F 214 " --> pdb=" O ALA F 203 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N PHE F 205 " --> pdb=" O VAL F 212 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 231 through 233 removed outlier: 3.528A pdb=" N VAL F 231 " --> pdb=" O THR F 238 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N GLU F 258 " --> pdb=" O ILE F 262 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N ILE F 262 " --> pdb=" O GLU F 258 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 276 through 283 removed outlier: 5.413A pdb=" N GLU F 277 " --> pdb=" O ARG F 292 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N ARG F 292 " --> pdb=" O GLU F 277 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 353 through 356 removed outlier: 7.060A pdb=" N ASN F 402 " --> pdb=" O GLY F 373 " (cutoff:3.500A) removed outlier: 9.770A pdb=" N GLU F 375 " --> pdb=" O ARG F 400 " (cutoff:3.500A) removed outlier: 10.552A pdb=" N ARG F 400 " --> pdb=" O GLU F 375 " (cutoff:3.500A) removed outlier: 11.361A pdb=" N PHE F 377 " --> pdb=" O VAL F 398 " (cutoff:3.500A) removed outlier: 13.405A pdb=" N VAL F 398 " --> pdb=" O PHE F 377 " (cutoff:3.500A) removed outlier: 15.427A pdb=" N VAL F 379 " --> pdb=" O VAL F 396 " (cutoff:3.500A) removed outlier: 16.185A pdb=" N VAL F 396 " --> pdb=" O VAL F 379 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 96 through 102 removed outlier: 3.696A pdb=" N GLY H 96 " --> pdb=" O THR H 449 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N VAL H 445 " --> pdb=" O PHE H 100 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N LYS H 102 " --> pdb=" O ILE H 443 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N ILE H 443 " --> pdb=" O LYS H 102 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N ARG H 420 " --> pdb=" O GLY H 448 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 115 through 124 removed outlier: 4.704A pdb=" N TRP H 115 " --> pdb=" O THR H 138 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N THR H 138 " --> pdb=" O TRP H 115 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N THR H 117 " --> pdb=" O GLN H 136 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N GLN H 136 " --> pdb=" O THR H 117 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N GLU H 119 " --> pdb=" O LEU H 134 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LEU H 134 " --> pdb=" O GLU H 119 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N THR H 157 " --> pdb=" O GLY H 135 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N LEU H 158 " --> pdb=" O VAL H 174 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LYS H 172 " --> pdb=" O MET H 160 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 179 through 184 removed outlier: 4.129A pdb=" N ASP H 197 " --> pdb=" O ASN H 200 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ALA H 201 " --> pdb=" O VAL H 216 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N VAL H 216 " --> pdb=" O ALA H 201 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ALA H 203 " --> pdb=" O SER H 214 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N SER H 214 " --> pdb=" O ALA H 203 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N PHE H 205 " --> pdb=" O VAL H 212 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 231 through 233 removed outlier: 3.524A pdb=" N VAL H 231 " --> pdb=" O THR H 238 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N GLU H 258 " --> pdb=" O ILE H 262 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N ILE H 262 " --> pdb=" O GLU H 258 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 276 through 283 removed outlier: 5.403A pdb=" N GLU H 277 " --> pdb=" O ARG H 292 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N ARG H 292 " --> pdb=" O GLU H 277 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 353 through 356 removed outlier: 7.058A pdb=" N ASN H 402 " --> pdb=" O GLY H 373 " (cutoff:3.500A) removed outlier: 9.765A pdb=" N GLU H 375 " --> pdb=" O ARG H 400 " (cutoff:3.500A) removed outlier: 10.533A pdb=" N ARG H 400 " --> pdb=" O GLU H 375 " (cutoff:3.500A) removed outlier: 11.375A pdb=" N PHE H 377 " --> pdb=" O VAL H 398 " (cutoff:3.500A) removed outlier: 13.429A pdb=" N VAL H 398 " --> pdb=" O PHE H 377 " (cutoff:3.500A) removed outlier: 15.440A pdb=" N VAL H 379 " --> pdb=" O VAL H 396 " (cutoff:3.500A) removed outlier: 16.201A pdb=" N VAL H 396 " --> pdb=" O VAL H 379 " (cutoff:3.500A) 443 hydrogen bonds defined for protein. 1176 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.47 Time building geometry restraints manager: 6.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2915 1.32 - 1.45: 3943 1.45 - 1.58: 8234 1.58 - 1.71: 0 1.71 - 1.84: 114 Bond restraints: 15206 Sorted by residual: bond pdb=" N GLY H 286 " pdb=" CA GLY H 286 " ideal model delta sigma weight residual 1.442 1.476 -0.034 7.70e-03 1.69e+04 1.96e+01 bond pdb=" CA SER F 279 " pdb=" CB SER F 279 " ideal model delta sigma weight residual 1.527 1.476 0.051 1.30e-02 5.92e+03 1.54e+01 bond pdb=" N THR G 153 " pdb=" CA THR G 153 " ideal model delta sigma weight residual 1.455 1.492 -0.038 9.60e-03 1.09e+04 1.53e+01 bond pdb=" N VAL C 68 " pdb=" CA VAL C 68 " ideal model delta sigma weight residual 1.457 1.501 -0.044 1.15e-02 7.56e+03 1.49e+01 bond pdb=" N THR H 153 " pdb=" CA THR H 153 " ideal model delta sigma weight residual 1.455 1.491 -0.037 9.60e-03 1.09e+04 1.46e+01 ... (remaining 15201 not shown) Histogram of bond angle deviations from ideal: 97.63 - 105.14: 263 105.14 - 112.65: 7555 112.65 - 120.16: 6899 120.16 - 127.67: 5749 127.67 - 135.18: 172 Bond angle restraints: 20638 Sorted by residual: angle pdb=" CA ASP G 125 " pdb=" CB ASP G 125 " pdb=" CG ASP G 125 " ideal model delta sigma weight residual 112.60 119.25 -6.65 1.00e+00 1.00e+00 4.42e+01 angle pdb=" N ILE H 397 " pdb=" CA ILE H 397 " pdb=" C ILE H 397 " ideal model delta sigma weight residual 111.67 106.10 5.57 9.50e-01 1.11e+00 3.43e+01 angle pdb=" N ILE E 397 " pdb=" CA ILE E 397 " pdb=" C ILE E 397 " ideal model delta sigma weight residual 111.67 106.19 5.48 9.50e-01 1.11e+00 3.33e+01 angle pdb=" N ILE G 397 " pdb=" CA ILE G 397 " pdb=" C ILE G 397 " ideal model delta sigma weight residual 111.67 106.34 5.33 9.50e-01 1.11e+00 3.14e+01 angle pdb=" N ILE F 397 " pdb=" CA ILE F 397 " pdb=" C ILE F 397 " ideal model delta sigma weight residual 111.67 106.36 5.31 9.50e-01 1.11e+00 3.12e+01 ... (remaining 20633 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.49: 9429 19.49 - 38.99: 512 38.99 - 58.48: 65 58.48 - 77.97: 48 77.97 - 97.46: 30 Dihedral angle restraints: 10084 sinusoidal: 5003 harmonic: 5081 Sorted by residual: dihedral pdb=" CA GLY G 297 " pdb=" C GLY G 297 " pdb=" N SER G 298 " pdb=" CA SER G 298 " ideal model delta harmonic sigma weight residual 180.00 150.02 29.98 0 5.00e+00 4.00e-02 3.59e+01 dihedral pdb=" CA GLY E 297 " pdb=" C GLY E 297 " pdb=" N SER E 298 " pdb=" CA SER E 298 " ideal model delta harmonic sigma weight residual 180.00 150.27 29.73 0 5.00e+00 4.00e-02 3.53e+01 dihedral pdb=" CA GLY H 297 " pdb=" C GLY H 297 " pdb=" N SER H 298 " pdb=" CA SER H 298 " ideal model delta harmonic sigma weight residual 180.00 150.44 29.56 0 5.00e+00 4.00e-02 3.50e+01 ... (remaining 10081 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 1701 0.095 - 0.190: 691 0.190 - 0.285: 88 0.285 - 0.380: 7 0.380 - 0.475: 4 Chirality restraints: 2491 Sorted by residual: chirality pdb=" C1 MAN k 4 " pdb=" O3 BMA k 3 " pdb=" C2 MAN k 4 " pdb=" O5 MAN k 4 " both_signs ideal model delta sigma weight residual False 2.40 2.24 0.16 2.00e-02 2.50e+03 6.36e+01 chirality pdb=" C1 NAG l 2 " pdb=" O4 NAG l 1 " pdb=" C2 NAG l 2 " pdb=" O5 NAG l 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-02 2.50e+03 4.66e+01 chirality pdb=" C1 FUC d 3 " pdb=" O6 NAG d 1 " pdb=" C2 FUC d 3 " pdb=" O5 FUC d 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.27 -0.13 2.00e-02 2.50e+03 4.19e+01 ... (remaining 2488 not shown) Planarity restraints: 2577 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG i 1 " -0.101 2.00e-02 2.50e+03 8.44e-02 8.91e+01 pdb=" C7 NAG i 1 " 0.047 2.00e-02 2.50e+03 pdb=" C8 NAG i 1 " -0.082 2.00e-02 2.50e+03 pdb=" N2 NAG i 1 " 0.128 2.00e-02 2.50e+03 pdb=" O7 NAG i 1 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG e 1 " 0.077 2.00e-02 2.50e+03 6.44e-02 5.19e+01 pdb=" C7 NAG e 1 " -0.039 2.00e-02 2.50e+03 pdb=" C8 NAG e 1 " 0.065 2.00e-02 2.50e+03 pdb=" N2 NAG e 1 " -0.095 2.00e-02 2.50e+03 pdb=" O7 NAG e 1 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG k 2 " -0.067 2.00e-02 2.50e+03 5.65e-02 3.99e+01 pdb=" C7 NAG k 2 " 0.033 2.00e-02 2.50e+03 pdb=" C8 NAG k 2 " -0.056 2.00e-02 2.50e+03 pdb=" N2 NAG k 2 " 0.085 2.00e-02 2.50e+03 pdb=" O7 NAG k 2 " 0.005 2.00e-02 2.50e+03 ... (remaining 2574 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 707 2.73 - 3.27: 14358 3.27 - 3.81: 25830 3.81 - 4.36: 36107 4.36 - 4.90: 55708 Nonbonded interactions: 132710 Sorted by model distance: nonbonded pdb=" O ASP E 293 " pdb="CA CA E 501 " model vdw 2.187 2.510 nonbonded pdb=" O HIS F 347 " pdb="CA CA F2000 " model vdw 2.217 2.510 nonbonded pdb=" O HIS G 347 " pdb="CA CA G2000 " model vdw 2.237 2.510 nonbonded pdb=" O HIS H 347 " pdb="CA CA H2000 " model vdw 2.280 2.510 nonbonded pdb=" O GLY F 345 " pdb="CA CA F2000 " model vdw 2.291 2.510 ... (remaining 132705 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain '1' selection = chain '2' selection = chain '4' selection = chain '5' selection = chain '6' selection = chain '7' selection = chain 'a' selection = chain 'b' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'i' selection = chain 'j' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'q' selection = chain 'r' selection = chain 't' selection = chain 'u' selection = chain 'v' selection = chain 'w' } ncs_group { reference = chain '3' selection = chain 'c' selection = chain 'k' selection = chain 's' } ncs_group { reference = (chain 'E' and (resid 82 through 469 or resid 501)) selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 13.930 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 38.450 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.240 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8972 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.061 15206 Z= 0.924 Angle : 1.671 8.304 20638 Z= 1.071 Chirality : 0.094 0.475 2491 Planarity : 0.011 0.084 2549 Dihedral : 14.040 97.465 6732 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 0.45 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.37 % Favored : 96.40 % Rotamer: Outliers : 0.06 % Allowed : 3.42 % Favored : 96.51 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 14.93 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.18), residues: 1778 helix: -0.48 (0.90), residues: 24 sheet: 0.26 (0.19), residues: 681 loop : -1.10 (0.17), residues: 1073 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.078 0.015 TRP G 115 HIS 0.033 0.007 HIS E 347 PHE 0.051 0.012 PHE E 205 TYR 0.076 0.014 TYR H 423 ARG 0.024 0.003 ARG G 156 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 140 time to evaluate : 1.514 Fit side-chains REVERT: E 150 ARG cc_start: 0.8672 (mtt180) cc_final: 0.8352 (mtp85) REVERT: G 199 LYS cc_start: 0.8992 (tttt) cc_final: 0.8715 (tptt) REVERT: B 4 MET cc_start: 0.8921 (mmm) cc_final: 0.8023 (mmm) REVERT: B 24 ARG cc_start: 0.8441 (ttt-90) cc_final: 0.8214 (mtm110) REVERT: B 27 GLN cc_start: 0.8411 (mt0) cc_final: 0.8185 (mp10) REVERT: B 92 ASN cc_start: 0.9181 (t0) cc_final: 0.8925 (t0) REVERT: C 100 ARG cc_start: 0.8570 (tpp80) cc_final: 0.8287 (tpp80) REVERT: C 116 GLU cc_start: 0.8708 (mt-10) cc_final: 0.8426 (mt-10) REVERT: C 125 THR cc_start: 0.8948 (m) cc_final: 0.8512 (p) REVERT: H 465 ASN cc_start: 0.9066 (m-40) cc_final: 0.8798 (m110) outliers start: 1 outliers final: 0 residues processed: 140 average time/residue: 1.4557 time to fit residues: 222.2940 Evaluate side-chains 101 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 1.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 146 optimal weight: 0.9990 chunk 131 optimal weight: 0.8980 chunk 73 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 88 optimal weight: 0.9990 chunk 70 optimal weight: 0.7980 chunk 136 optimal weight: 0.6980 chunk 52 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 158 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 393 ASN C 120 GLN F 465 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8922 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15206 Z= 0.218 Angle : 0.674 8.528 20638 Z= 0.359 Chirality : 0.048 0.203 2491 Planarity : 0.003 0.033 2549 Dihedral : 9.151 74.339 3589 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.14 % Favored : 97.64 % Rotamer: Outliers : 1.03 % Allowed : 6.59 % Favored : 92.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.93 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.19), residues: 1778 helix: -0.06 (0.95), residues: 24 sheet: 0.50 (0.19), residues: 676 loop : -0.52 (0.18), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP H 178 HIS 0.008 0.001 HIS E 336 PHE 0.016 0.002 PHE E 132 TYR 0.023 0.002 TYR B 91 ARG 0.003 0.000 ARG F 288 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 116 time to evaluate : 1.729 Fit side-chains revert: symmetry clash REVERT: B 27 GLN cc_start: 0.8436 (mt0) cc_final: 0.8072 (mp10) REVERT: B 70 GLU cc_start: 0.8375 (tp30) cc_final: 0.8161 (mm-30) REVERT: C 78 THR cc_start: 0.8489 (m) cc_final: 0.7924 (p) REVERT: C 125 THR cc_start: 0.8900 (m) cc_final: 0.8650 (p) REVERT: H 467 MET cc_start: 0.8061 (ptm) cc_final: 0.7819 (ptm) outliers start: 16 outliers final: 7 residues processed: 124 average time/residue: 1.4106 time to fit residues: 192.2513 Evaluate side-chains 100 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 93 time to evaluate : 1.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 151 ASP Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain H residue 128 LYS Chi-restraints excluded: chain H residue 151 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 87 optimal weight: 10.0000 chunk 49 optimal weight: 3.9990 chunk 131 optimal weight: 0.5980 chunk 107 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 158 optimal weight: 0.9990 chunk 171 optimal weight: 0.7980 chunk 140 optimal weight: 0.7980 chunk 156 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 126 optimal weight: 4.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8916 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15206 Z= 0.201 Angle : 0.607 9.328 20638 Z= 0.318 Chirality : 0.046 0.183 2491 Planarity : 0.003 0.047 2549 Dihedral : 8.134 64.232 3589 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.08 % Favored : 97.69 % Rotamer: Outliers : 1.10 % Allowed : 8.27 % Favored : 90.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.93 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.19), residues: 1778 helix: 0.09 (0.97), residues: 24 sheet: 0.52 (0.19), residues: 696 loop : -0.38 (0.18), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP H 178 HIS 0.009 0.001 HIS F 336 PHE 0.015 0.002 PHE E 410 TYR 0.018 0.002 TYR B 91 ARG 0.006 0.000 ARG B 24 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 115 time to evaluate : 1.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 230 CYS cc_start: 0.8712 (OUTLIER) cc_final: 0.8489 (p) REVERT: B 24 ARG cc_start: 0.8635 (mtp-110) cc_final: 0.8399 (mtp-110) REVERT: B 70 GLU cc_start: 0.8571 (tp30) cc_final: 0.8364 (mm-30) REVERT: B 98 THR cc_start: 0.9184 (m) cc_final: 0.8805 (p) REVERT: C 11 VAL cc_start: 0.8805 (OUTLIER) cc_final: 0.8533 (t) REVERT: C 125 THR cc_start: 0.8926 (m) cc_final: 0.8590 (p) REVERT: H 400 ARG cc_start: 0.8403 (ptp-110) cc_final: 0.8160 (ptm160) outliers start: 17 outliers final: 6 residues processed: 127 average time/residue: 1.2421 time to fit residues: 175.3299 Evaluate side-chains 109 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 101 time to evaluate : 1.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 151 ASP Chi-restraints excluded: chain E residue 230 CYS Chi-restraints excluded: chain G residue 230 CYS Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain F residue 230 CYS Chi-restraints excluded: chain H residue 151 ASP Chi-restraints excluded: chain H residue 230 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 156 optimal weight: 3.9990 chunk 119 optimal weight: 0.9980 chunk 82 optimal weight: 9.9990 chunk 17 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 106 optimal weight: 0.0770 chunk 158 optimal weight: 0.9990 chunk 168 optimal weight: 0.9980 chunk 150 optimal weight: 0.0020 chunk 45 optimal weight: 0.9980 chunk 140 optimal weight: 0.2980 overall best weight: 0.4746 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8888 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 15206 Z= 0.157 Angle : 0.569 9.977 20638 Z= 0.294 Chirality : 0.045 0.197 2491 Planarity : 0.003 0.040 2549 Dihedral : 7.243 53.714 3589 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.22 % Allowed : 1.86 % Favored : 97.92 % Rotamer: Outliers : 1.03 % Allowed : 10.01 % Favored : 88.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.93 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.19), residues: 1778 helix: 0.46 (1.02), residues: 24 sheet: 0.60 (0.19), residues: 694 loop : -0.22 (0.19), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 178 HIS 0.004 0.001 HIS F 274 PHE 0.013 0.002 PHE G 410 TYR 0.017 0.001 TYR B 91 ARG 0.003 0.000 ARG B 54 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 114 time to evaluate : 1.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 103 ASP cc_start: 0.8638 (p0) cc_final: 0.8356 (p0) REVERT: E 400 ARG cc_start: 0.8818 (ptp-110) cc_final: 0.8537 (ptm160) REVERT: B 5 THR cc_start: 0.9019 (m) cc_final: 0.8781 (p) REVERT: B 24 ARG cc_start: 0.8585 (mtp-110) cc_final: 0.8296 (mtp-110) REVERT: B 98 THR cc_start: 0.9211 (m) cc_final: 0.8862 (p) REVERT: C 11 VAL cc_start: 0.8796 (OUTLIER) cc_final: 0.8539 (t) REVERT: C 78 THR cc_start: 0.8590 (m) cc_final: 0.8074 (p) REVERT: C 125 THR cc_start: 0.8942 (m) cc_final: 0.8590 (p) REVERT: H 400 ARG cc_start: 0.8410 (ptp-110) cc_final: 0.8157 (ptm160) outliers start: 16 outliers final: 7 residues processed: 123 average time/residue: 1.3349 time to fit residues: 182.3434 Evaluate side-chains 110 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 102 time to evaluate : 1.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 151 ASP Chi-restraints excluded: chain E residue 230 CYS Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain F residue 230 CYS Chi-restraints excluded: chain H residue 151 ASP Chi-restraints excluded: chain H residue 230 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 95 optimal weight: 9.9990 chunk 2 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 143 optimal weight: 0.8980 chunk 116 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 85 optimal weight: 0.8980 chunk 150 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 56 optimal weight: 0.7980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8928 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15206 Z= 0.256 Angle : 0.598 9.772 20638 Z= 0.308 Chirality : 0.046 0.211 2491 Planarity : 0.003 0.042 2549 Dihedral : 7.284 55.421 3589 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.36 % Favored : 97.41 % Rotamer: Outliers : 1.49 % Allowed : 10.21 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.93 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.19), residues: 1778 helix: 0.38 (1.05), residues: 24 sheet: 0.46 (0.19), residues: 695 loop : -0.23 (0.19), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 178 HIS 0.005 0.001 HIS F 336 PHE 0.015 0.002 PHE E 410 TYR 0.021 0.002 TYR B 91 ARG 0.003 0.000 ARG B 24 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 105 time to evaluate : 1.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 98 THR cc_start: 0.9240 (m) cc_final: 0.8910 (p) REVERT: C 11 VAL cc_start: 0.8805 (OUTLIER) cc_final: 0.8538 (t) REVERT: C 78 THR cc_start: 0.8553 (m) cc_final: 0.8040 (p) REVERT: C 125 THR cc_start: 0.8938 (m) cc_final: 0.8526 (p) REVERT: H 400 ARG cc_start: 0.8447 (ptp-110) cc_final: 0.8199 (ptm160) outliers start: 23 outliers final: 11 residues processed: 120 average time/residue: 1.2873 time to fit residues: 171.2254 Evaluate side-chains 116 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 104 time to evaluate : 1.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 151 ASP Chi-restraints excluded: chain E residue 230 CYS Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain G residue 83 GLU Chi-restraints excluded: chain G residue 148 THR Chi-restraints excluded: chain G residue 390 LEU Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain F residue 230 CYS Chi-restraints excluded: chain H residue 151 ASP Chi-restraints excluded: chain H residue 230 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 151 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 98 optimal weight: 4.9990 chunk 41 optimal weight: 0.0870 chunk 168 optimal weight: 0.6980 chunk 139 optimal weight: 3.9990 chunk 77 optimal weight: 20.0000 chunk 13 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 chunk 162 optimal weight: 4.9990 overall best weight: 0.8960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8918 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 15206 Z= 0.212 Angle : 0.583 10.346 20638 Z= 0.299 Chirality : 0.046 0.214 2491 Planarity : 0.003 0.043 2549 Dihedral : 7.077 52.842 3589 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.14 % Favored : 97.64 % Rotamer: Outliers : 1.10 % Allowed : 11.11 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.93 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.19), residues: 1778 helix: 0.49 (1.09), residues: 24 sheet: 0.42 (0.19), residues: 697 loop : -0.21 (0.19), residues: 1057 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 178 HIS 0.003 0.001 HIS E 336 PHE 0.014 0.002 PHE E 410 TYR 0.017 0.002 TYR B 91 ARG 0.008 0.000 ARG B 24 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 109 time to evaluate : 1.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 400 ARG cc_start: 0.8848 (ptp-110) cc_final: 0.8572 (ptm160) REVERT: B 98 THR cc_start: 0.9241 (m) cc_final: 0.8920 (p) REVERT: C 11 VAL cc_start: 0.8808 (OUTLIER) cc_final: 0.8548 (t) REVERT: C 78 THR cc_start: 0.8653 (m) cc_final: 0.8143 (p) REVERT: C 125 THR cc_start: 0.8940 (m) cc_final: 0.8525 (p) REVERT: H 400 ARG cc_start: 0.8453 (ptp-110) cc_final: 0.8202 (ptm160) REVERT: H 465 ASN cc_start: 0.9032 (m110) cc_final: 0.8752 (m110) outliers start: 17 outliers final: 12 residues processed: 121 average time/residue: 1.2121 time to fit residues: 163.0713 Evaluate side-chains 113 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 100 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 151 ASP Chi-restraints excluded: chain E residue 230 CYS Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain G residue 148 THR Chi-restraints excluded: chain G residue 390 LEU Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain F residue 230 CYS Chi-restraints excluded: chain H residue 148 THR Chi-restraints excluded: chain H residue 151 ASP Chi-restraints excluded: chain H residue 230 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 18 optimal weight: 0.0050 chunk 95 optimal weight: 10.0000 chunk 122 optimal weight: 0.6980 chunk 141 optimal weight: 4.9990 chunk 94 optimal weight: 0.9980 chunk 167 optimal weight: 2.9990 chunk 104 optimal weight: 0.7980 chunk 102 optimal weight: 0.7980 chunk 77 optimal weight: 7.9990 chunk 103 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 141 ASN B 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8904 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15206 Z= 0.177 Angle : 0.565 10.485 20638 Z= 0.288 Chirality : 0.045 0.215 2491 Planarity : 0.003 0.042 2549 Dihedral : 6.749 48.743 3589 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.59 % Favored : 97.19 % Rotamer: Outliers : 1.49 % Allowed : 11.05 % Favored : 87.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.93 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.20), residues: 1778 helix: 0.52 (1.08), residues: 24 sheet: 0.36 (0.19), residues: 717 loop : -0.08 (0.19), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 178 HIS 0.002 0.001 HIS F 274 PHE 0.013 0.002 PHE E 410 TYR 0.017 0.001 TYR B 91 ARG 0.006 0.000 ARG B 24 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 106 time to evaluate : 1.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 400 ARG cc_start: 0.8826 (ptp-110) cc_final: 0.8553 (ptm160) REVERT: B 98 THR cc_start: 0.9243 (m) cc_final: 0.8935 (p) REVERT: C 11 VAL cc_start: 0.8815 (OUTLIER) cc_final: 0.8572 (t) REVERT: C 78 THR cc_start: 0.8608 (m) cc_final: 0.8084 (p) REVERT: C 125 THR cc_start: 0.8932 (m) cc_final: 0.8515 (p) REVERT: F 368 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.8167 (mp0) REVERT: H 400 ARG cc_start: 0.8444 (ptp-110) cc_final: 0.8178 (ptm160) REVERT: H 465 ASN cc_start: 0.9008 (m110) cc_final: 0.8732 (m110) outliers start: 23 outliers final: 9 residues processed: 123 average time/residue: 1.1968 time to fit residues: 164.2359 Evaluate side-chains 115 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 104 time to evaluate : 1.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 151 ASP Chi-restraints excluded: chain E residue 230 CYS Chi-restraints excluded: chain G residue 148 THR Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain F residue 230 CYS Chi-restraints excluded: chain F residue 368 GLU Chi-restraints excluded: chain H residue 148 THR Chi-restraints excluded: chain H residue 151 ASP Chi-restraints excluded: chain H residue 230 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 100 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 106 optimal weight: 0.9980 chunk 114 optimal weight: 6.9990 chunk 82 optimal weight: 9.9990 chunk 15 optimal weight: 0.8980 chunk 131 optimal weight: 1.9990 chunk 152 optimal weight: 6.9990 chunk 160 optimal weight: 0.9980 chunk 146 optimal weight: 0.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 141 ASN B 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8932 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 15206 Z= 0.261 Angle : 0.598 10.544 20638 Z= 0.306 Chirality : 0.046 0.228 2491 Planarity : 0.003 0.043 2549 Dihedral : 6.984 51.854 3589 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.64 % Favored : 97.13 % Rotamer: Outliers : 1.42 % Allowed : 11.11 % Favored : 87.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.93 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.19), residues: 1778 helix: 0.50 (1.10), residues: 24 sheet: 0.30 (0.19), residues: 717 loop : -0.16 (0.19), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 178 HIS 0.003 0.001 HIS F 336 PHE 0.015 0.002 PHE E 410 TYR 0.017 0.002 TYR B 91 ARG 0.006 0.000 ARG B 24 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 103 time to evaluate : 1.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 400 ARG cc_start: 0.8863 (ptp-110) cc_final: 0.8599 (ptm160) REVERT: G 344 GLU cc_start: 0.8806 (OUTLIER) cc_final: 0.7863 (mp0) REVERT: B 98 THR cc_start: 0.9260 (m) cc_final: 0.8952 (p) REVERT: C 11 VAL cc_start: 0.8835 (OUTLIER) cc_final: 0.8577 (t) REVERT: C 78 THR cc_start: 0.8623 (m) cc_final: 0.8095 (p) REVERT: C 125 THR cc_start: 0.8896 (m) cc_final: 0.8459 (p) REVERT: H 400 ARG cc_start: 0.8459 (ptp-110) cc_final: 0.8200 (ptm160) REVERT: H 465 ASN cc_start: 0.9017 (m110) cc_final: 0.8728 (m110) outliers start: 22 outliers final: 13 residues processed: 119 average time/residue: 1.2139 time to fit residues: 161.0678 Evaluate side-chains 115 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 100 time to evaluate : 1.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 151 ASP Chi-restraints excluded: chain E residue 230 CYS Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain G residue 148 THR Chi-restraints excluded: chain G residue 344 GLU Chi-restraints excluded: chain G residue 390 LEU Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain F residue 230 CYS Chi-restraints excluded: chain H residue 148 THR Chi-restraints excluded: chain H residue 151 ASP Chi-restraints excluded: chain H residue 230 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 156 optimal weight: 0.8980 chunk 160 optimal weight: 0.6980 chunk 94 optimal weight: 0.9980 chunk 68 optimal weight: 0.0010 chunk 122 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 chunk 141 optimal weight: 3.9990 chunk 147 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 102 optimal weight: 0.7980 chunk 165 optimal weight: 1.9990 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 141 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8903 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15206 Z= 0.169 Angle : 0.567 10.666 20638 Z= 0.289 Chirality : 0.045 0.214 2491 Planarity : 0.003 0.042 2549 Dihedral : 6.633 48.993 3589 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.31 % Favored : 97.47 % Rotamer: Outliers : 1.16 % Allowed : 11.95 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.93 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.20), residues: 1778 helix: 0.54 (1.09), residues: 24 sheet: 0.34 (0.19), residues: 717 loop : -0.09 (0.19), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 178 HIS 0.002 0.001 HIS E 144 PHE 0.013 0.002 PHE E 410 TYR 0.017 0.001 TYR B 91 ARG 0.010 0.000 ARG B 24 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 105 time to evaluate : 1.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 344 GLU cc_start: 0.8796 (OUTLIER) cc_final: 0.7853 (mp0) REVERT: B 98 THR cc_start: 0.9260 (m) cc_final: 0.8960 (p) REVERT: C 11 VAL cc_start: 0.8832 (OUTLIER) cc_final: 0.8585 (t) REVERT: C 78 THR cc_start: 0.8637 (m) cc_final: 0.8101 (p) REVERT: C 125 THR cc_start: 0.8893 (m) cc_final: 0.8451 (p) REVERT: H 400 ARG cc_start: 0.8444 (ptp-110) cc_final: 0.8172 (ptm160) REVERT: H 465 ASN cc_start: 0.9004 (m110) cc_final: 0.8733 (m110) outliers start: 18 outliers final: 12 residues processed: 117 average time/residue: 1.2296 time to fit residues: 160.2319 Evaluate side-chains 116 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 102 time to evaluate : 1.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 151 ASP Chi-restraints excluded: chain E residue 230 CYS Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain G residue 148 THR Chi-restraints excluded: chain G residue 344 GLU Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain F residue 230 CYS Chi-restraints excluded: chain H residue 148 THR Chi-restraints excluded: chain H residue 151 ASP Chi-restraints excluded: chain H residue 230 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 100 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 114 optimal weight: 6.9990 chunk 173 optimal weight: 0.8980 chunk 159 optimal weight: 0.8980 chunk 138 optimal weight: 0.6980 chunk 14 optimal weight: 4.9990 chunk 106 optimal weight: 0.8980 chunk 84 optimal weight: 5.9990 chunk 109 optimal weight: 0.9980 chunk 147 optimal weight: 4.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 141 ASN B 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8915 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15206 Z= 0.210 Angle : 0.573 10.758 20638 Z= 0.293 Chirality : 0.045 0.223 2491 Planarity : 0.003 0.045 2549 Dihedral : 6.668 49.391 3589 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.47 % Favored : 97.30 % Rotamer: Outliers : 0.97 % Allowed : 12.08 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.93 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.20), residues: 1778 helix: 0.51 (1.09), residues: 24 sheet: 0.33 (0.19), residues: 717 loop : -0.11 (0.19), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 178 HIS 0.002 0.001 HIS F 336 PHE 0.014 0.002 PHE E 410 TYR 0.015 0.002 TYR B 91 ARG 0.010 0.000 ARG B 24 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 107 time to evaluate : 1.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 400 ARG cc_start: 0.8901 (ptp-110) cc_final: 0.8636 (ptm160) REVERT: G 344 GLU cc_start: 0.8791 (OUTLIER) cc_final: 0.7814 (mp0) REVERT: B 98 THR cc_start: 0.9265 (m) cc_final: 0.8970 (p) REVERT: C 11 VAL cc_start: 0.8846 (OUTLIER) cc_final: 0.8595 (t) REVERT: C 78 THR cc_start: 0.8643 (m) cc_final: 0.8105 (p) REVERT: C 125 THR cc_start: 0.8889 (m) cc_final: 0.8443 (p) REVERT: F 368 GLU cc_start: 0.8470 (mp0) cc_final: 0.8186 (mp0) REVERT: H 400 ARG cc_start: 0.8456 (ptp-110) cc_final: 0.8180 (ptm160) REVERT: H 465 ASN cc_start: 0.9012 (m110) cc_final: 0.8743 (m110) outliers start: 15 outliers final: 12 residues processed: 118 average time/residue: 1.2270 time to fit residues: 161.2547 Evaluate side-chains 117 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 103 time to evaluate : 1.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 151 ASP Chi-restraints excluded: chain E residue 230 CYS Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain G residue 148 THR Chi-restraints excluded: chain G residue 344 GLU Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain F residue 230 CYS Chi-restraints excluded: chain H residue 148 THR Chi-restraints excluded: chain H residue 151 ASP Chi-restraints excluded: chain H residue 230 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 42 optimal weight: 1.9990 chunk 127 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 38 optimal weight: 0.5980 chunk 138 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 141 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 121 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 141 ASN B 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.092854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.069494 restraints weight = 22601.530| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 2.34 r_work: 0.2792 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2680 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15206 Z= 0.192 Angle : 0.567 10.664 20638 Z= 0.289 Chirality : 0.045 0.220 2491 Planarity : 0.003 0.045 2549 Dihedral : 6.578 49.563 3589 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.59 % Favored : 97.19 % Rotamer: Outliers : 1.03 % Allowed : 12.14 % Favored : 86.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.93 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.20), residues: 1778 helix: 0.55 (1.09), residues: 24 sheet: 0.34 (0.19), residues: 717 loop : -0.10 (0.20), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 178 HIS 0.002 0.001 HIS F 336 PHE 0.014 0.002 PHE E 410 TYR 0.016 0.002 TYR B 91 ARG 0.011 0.000 ARG B 24 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4354.32 seconds wall clock time: 78 minutes 54.06 seconds (4734.06 seconds total)